From d981fd01b88c643196bc0eb6f44035a5f7477cfc Mon Sep 17 00:00:00 2001 From: Eric Banks Date: Thu, 2 May 2013 15:18:13 -0400 Subject: [PATCH] Now that we don't generate dict and fai files, the resource script needs to copy them to the bundle. --- .../queue/qscripts/GATKResourcesBundle.scala | 25 +++++++++++-------- 1 file changed, 15 insertions(+), 10 deletions(-) diff --git a/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/GATKResourcesBundle.scala b/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/GATKResourcesBundle.scala index ad83ac723..1736adc17 100644 --- a/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/GATKResourcesBundle.scala +++ b/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/GATKResourcesBundle.scala @@ -234,8 +234,7 @@ class GATKResourcesBundle extends QScript { for ( resource: Resource <- RESOURCES ) { if ( isFASTA(resource.file) ) { - val f = copyBundleFile(resource, resource.ref) - add(new createDictandFAI(f)) + copyBundleFasta(resource, resource.ref) } else if ( isBAM(resource.file) ) { val f = copyBundleFile(resource, resource.ref) add(new IndexBAM(f)) @@ -312,6 +311,20 @@ class GATKResourcesBundle extends QScript { } } + def copyBundleFasta(res: Resource, ref: Reference) { + val out = destFile(BUNDLE_DIR, ref, res.destname(ref)) + add(new cpFile(res.file, out)) + + val oldRefDict = swapExt(res.file.getParent, res.file, ".fasta", ".dict") + val newRefDict = swapExt(out.getParent, out, ".fasta", ".dict") + + val oldRefFai = swapExt(res.file.getParent, res.file, ".fasta", ".fasta.fai") + val newRefFai = swapExt(out.getParent, out, ".fasta", ".fasta.fai") + + add(new cpFile(oldRefDict, newRefDict)) + add(new cpFile(oldRefFai, newRefFai)) + } + def copyBundleFile(res: Resource, ref: Reference): File = { val out = destFile(BUNDLE_DIR, ref, res.destname(ref)) add(new cpFile(res.file, out)) @@ -389,13 +402,5 @@ class GATKResourcesBundle extends QScript { else return ""; } - - class createDictandFAI (@Input ref: File) extends FastaStats with UNIVERSAL_GATK_ARGS { - @Output val outDict: File = swapExt(ref.getParent, ref, ".fasta", ".dict") - @Output val outFai: File = swapExt(ref.getParent, ref, ".fasta", ".fasta.fai") - @Output val outStats: File = swapExt(ref.getParent, ref, ".fasta", ".stats") - this.reference_sequence = ref - this.out = outStats - } }